Does this stem from a change in probtrackx or has this always been a deficiency of the interface?

I think probtrackx has always been like that

Sorry, I don't know what you're saying "yes" to.

I think probtrackx has always been like that, sry I misread your question and I was updating my reply

I've found some other similar little inconsistencies. It's ok if I propose other pull requests or do you prefer that I just open issues? I'm not too practiced in git

Due to the low maintenance level in nipype (nobody has much time to spend on it), it's probably most efficient to open PRs unless it would be more costly to attempt to fix things before discussing them.

It may also be most efficient to copy/fix interfaces in the packages that use them, so that you are not dependent on our release cycle, which is basically unspecified at this point. Anyway, thanks for this.